chr10-130160871-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006541.5(GLRX3):āc.352A>Gā(p.Ser118Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,609,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S118N) has been classified as Uncertain significance.
Frequency
Consequence
NM_006541.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRX3 | NM_006541.5 | c.352A>G | p.Ser118Gly | missense_variant | 4/11 | ENST00000331244.10 | |
GLRX3 | NM_001199868.2 | c.352A>G | p.Ser118Gly | missense_variant | 4/12 | ||
GLRX3 | NM_001321980.2 | c.-87A>G | 5_prime_UTR_variant | 5/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRX3 | ENST00000331244.10 | c.352A>G | p.Ser118Gly | missense_variant | 4/11 | 1 | NM_006541.5 | P1 | |
GLRX3 | ENST00000481034.1 | c.352A>G | p.Ser118Gly | missense_variant, NMD_transcript_variant | 4/13 | 1 | |||
GLRX3 | ENST00000368644.5 | c.352A>G | p.Ser118Gly | missense_variant | 4/12 | 2 | P1 | ||
GLRX3 | ENST00000486974.1 | n.240A>G | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251474Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135912
GnomAD4 exome AF: 0.0000268 AC: 39AN: 1457698Hom.: 0 Cov.: 29 AF XY: 0.0000345 AC XY: 25AN XY: 725516
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.352A>G (p.S118G) alteration is located in exon 4 (coding exon 4) of the GLRX3 gene. This alteration results from a A to G substitution at nucleotide position 352, causing the serine (S) at amino acid position 118 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at